Moving to the Dark Side

Leaving the Pipette for a Keyboard.

Install bioconductor packages from SVN

Due to some issues with the way DEXseq calculates the log2foldchanges I decided to re-run an analysis with the issue fixed. Since it is not yet in the development branch, an install from svn was needed - my first!

Firstly the source code was downloaded with:

  
svn co --username readonly --password readonly https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DEXSeq DEXSeq

This followed a build to generated a package:

  
R CMD build --no-build-vignettes DEXSeq

I had issues with the build process, which failed during the vignette build. As I don’t care about it, using --no-build-vignettes bypassed the problem. Then it was a simply matter of starting R and installing the package:

  
install.packages("DEXSeq_1.12.2.tar.gz", repos=NULL)

Simple.